edwards.oats {agridat}R Documentation

Multi-environment trial of oats in United States, 5 locations, 7 years.

Description

Multi-environment trial of oats in 5 locations, 7 years, with 3 replicates in each trial.

Usage

data("edwards.oats")

Format

A data frame with 3694 observations on the following 7 variables.

eid

Environment identification (factor)

year

Year

loc

Location name

block

Block

gen

Genotype name

yield

Yield

testwt

Test weight

Details

This data comes from a breeding program, but does not have the usual pattern of (1) genotypes entering/leaving the program (2) check genotypes that remain throughout the duration of the program.

Experiments were conducted by the Iowa State University Oat Variety Trial in the years 1997 to 2003.

In each year there were 40 genotypes, with about 30 released checks and 10 experimental lines. Each genotype appeared in a range of 3 to 34 of the year-loc combinations.

The trials were grown in five locations in Iowa: Ames, Nashua, Crawfordsville, Lewis, Sutherland. In 1998 there was no trial grown at Sutherland. There were 3 blocks in each trial.

Five genotypes were removed from the data because of low yields (and are not included here).

The environment identifaction values are the same as in Edwards (2006) table 1.

Electronic data supplied by Jode Edwards.

Source

Jode W. Edwards, Jean-Luc Jannink (2006). Bayesian Modeling of Heterogeneous Error and Genotype x Environment Interaction Variances. Crop Science, 46, 820-833. https://dx.doi.org/10.2135/cropsci2005.0164

References

None

Examples

## Not run: 

  library(agridat)
  libs(dplyr,lattice, reshape2, stringr)
  data(edwards.oats)
  dat <- edwards.oats
  dat$env <- paste0(dat$year,".",dat$loc)
  dat$eid <- factor(dat$eid)
  mat <- reshape2::acast(dat, env ~ gen,
                         fun.aggregate=mean, value.var="yield", na.rm=TRUE)
  lattice::levelplot(mat, aspect="m",
                     main="edwards.oats",
                     xlab="environment", ylab="genotype",
                     scales=list(x=list(rot=90)))

  # Calculate BLUEs of gen/env effects
  m1 <- lm(yield ~ gen+eid, dat)

  gg <- coef(m1)[2:80]
  names(gg) <- stringr::str_replace(names(gg), "gen", "")
  gg <- c(0,gg)
  names(gg)[1] <- "ACStewart"

  ee <- coef(m1)[81:113]
  names(ee) <- stringr::str_replace(names(ee), "eid", "")
  ee <- c(0,ee)
  names(ee)[1] <- "1"
  
  # Subtract gen/env coefs from yield values
  dat2 <- dat
  dat2$gencoef <- gg[match(dat2$gen, names(gg))]
  dat2$envcoef <- ee[match(dat2$eid, names(ee))]
  dat2 <- dplyr::mutate(dat2, y = yield - gencoef - envcoef)

  # Calculate variance for each gen*env. Shape of the graph is vaguely
  # similar to Fig 2 of Edwards et al (2006), who used a Bayesian model
  dat2 <- group_by(dat2, gen, eid)
  dat2sum <- summarize(dat2, stddev = sd(y))
  bwplot(stddev ~ eid, dat2sum)


## End(Not run)

[Package agridat version 1.18 Index]